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Update `batch_single_subject.sh` for the 2025 SCT Course - #33

Merged

joshuacwnewton merged 22 commits into

masterfrom

jn/update-for-2025-sct-course

Dec 4, 2025

Merged

Update `batch_single_subject.sh` for the 2025 SCT Course#33
joshuacwnewton merged 22 commits into
masterfrom
jn/update-for-2025-sct-course

Commits on Nov 18, 2025
- Temporarily turn off PR trigger on workflows
  joshuacwnewton
  committed
  5ca1c2a
- Add GHA workflow to diff slides with batch script
  joshuacwnewton
  committed
  bd48328
Commits on Nov 19, 2025
- Replace `sct_label_vertebrae` with disc labels from `totalspineseg`
  joshuacwnewton
  committed
  33fcc22
- Replace `sct_deepseg_gm` with `sct_deepseg graymatter`
  joshuacwnewton
  committed
  a6d80ca
- Replace `sct_deepseg_sc` with `sct_deepseg spinalcord`
  joshuacwnewton
  committed
  06c0161
- Add missing lumbar `sct_qc` command
  joshuacwnewton
  committed
  b31a5bd
- Uncomment `sct_analyze_lesion -f` command
  joshuacwnewton
  committed
  bd6c4c1
- Add space to commented-out `sct_label_utils` command
  joshuacwnewton
  committed
  0eb1aec
- Add new `sct_compute_ascor` command
  joshuacwnewton
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  4ab8bbc
- Temporarily commit course text to make testing easier
  joshuacwnewton
  committed
  53665c3
- Revert "Temporarily commit course text to make testing easier"
  joshuacwnewton
  committed
  3c42572
- Revert "Temporarily turn off PR trigger on workflows"
  joshuacwnewton
  committed
  bfe9286
- Fix `-step1-only` syntax
  joshuacwnewton
  committed
  c98f50b
- `gmseg` -> `gm_seg` to match new `graymatter` output
  joshuacwnewton
  committed
  8812617
- `batch_single_subject.sh`: Fix `aSCOR` typo (`-1` -> `1`)
  joshuacwnewton
  committed
  cd149da
- `batch_single_subject.sh`: Revert back to `_gmseg`
  joshuacwnewton
  committed
  60ebdeb
Commits on Nov 20, 2025
- `batch_single_subject.sh`: Add cmd to generate `t2_seg_labeled.nii.gz`
  joshuacwnewton
  committed
  e51c8fb
- `batch_single_subject.sh`: Remove sct_label_vertebrae comments
  joshuacwnewton
  committed
  dc8264a
Commits on Nov 28, 2025
- `batch_single_subject.sh`: Update totalspineseg syntax/output fname
  joshuacwnewton
  committed
  aa88fb2
- `batch_single_subject.sh`: Update tutorial-specific command
  joshuacwnewton
  committed
  8719e48
Commits on Dec 2, 2025
- `batch_single_subject.sh`: Add cropping step to improve `sc_epi`
  joshuacwnewton
  committed
  fd6d63d
- `run_script_and_create_release.yml`: Upload QC artifact
  joshuacwnewton
  committed
  93cddf5

Commits

Commits on Nov 18, 2025

Commits on Nov 19, 2025

Commits on Nov 20, 2025

Commits on Nov 28, 2025

Commits on Dec 2, 2025